Manchester United's new manager David Moyes is facing his first headache even before his expected appointment today, as it has emerged that Wayne Rooney has told the club that he believes he needs a fresh start and wants to leave.

Rooney is understood to have met Six Alex Ferguson two weeks ago and told the Scot, who announced his retirement as United manager yesterday, that he wants to leave the club. Ferguson categorically rejected that request and though the club say they do not want to sell, the player's £250,000-a-week contract which has two years left to run will be difficult to renew at the same level, following Rooney's performance levels of this season. United stated: “Wayne Rooney is not for sale.”

The 27-year-old, who will now be asked to work for a new manager who sued him over comments he made in his 2006 autobiography, did not know of Ferguson's intention to leave when he asked to go and Moyes' imminent arrival has not been a factor in his request.

Ferguson has dropped Rooney into a deep-lying midfield role which ill-suited him this season and said publicly that he must fight with Shinji Kagawa for a place behind the striker. Though their relationship is believed to have improved since Rooney was omitted from the side to face Real Madrid in the Champions League last 16 match at Old Trafford, he has been linked with Bayern Munich.

A meeting between outgoing chief executive David Gill and Cristiano Ronaldo's agent, Jorge Mendes, has also given rise to fresh suggestions that Ronaldo may be in line for an £80m return to Manchester, though Gill is no longer conducting transfer business, ahead of his own departure from United on June 30.

United's appointment of Moyes as Sir Alex Ferguson' successor is likely to be confirmed after the 50-year-old has met Everton's players at training later this morning, after weeks of work under a cloak of secrecy by the club to ensure a smooth transition at Old Trafford.

Ferguson’s decision to retire, bringing the curtain down on an extraordinary 26 years at United, was confirmed at 9.15am today, the Scot’s one last frustration with the national print media being that it beat the club to news Old Trafford had planned to announce at 10am.

Moyes’ move at the end of the season already leaves Wigan Athletic’s Roberto Martinez, former Everton player Mark Hughes, whose agent Kia Joorabchian has close links to club chairman Bill Kenwright, and Martin O’Neill as potential successors at Goodison. But it also leaves Everton aggrieved that United have not approached them directly about the imminent appointment. Moyes is understood only to have told his chairman Bill Kenwright at 1.30pm. He did not discuss his appointment with Everton’s players when he took training today and travelled to London with his brother and agent, Kenny, to watch Chelsea play Tottenham Hotspur.

The Independent understands that United consider Jose Mourinho’s appointment as Chelsea’s manager this summer to be a certainty. But 50-year-old Moyes, who may bring his captain Phil Neville with him to Old Trafford in a coaching role, has been No 1 on United’s list since Ferguson announced his intention to retire in late February. Gill and the Glazer family did not try to dissuade him.

Ferguson’s own input concerning the choice is said to have been “critical”. Moyes is expected to take the club he has managed for 11 years to West Ham on Sunday and his customary Friday press conference has not been cancelled – as Ferguson’s has. But with Moyes out of contract on 30 June, agreeing a deal with him is the only hurdle for United’s chief executive designate, Ed Woodward – who is leading discussions. Moyes is expected formally to take over as United manager on 1 July.

Woodward and the current chief executive David Gill, who will step down on the same day as Ferguson, are adamant that the new manager will be allowed to bring in two or three new players, rather than overhaul the side. That philosophy weighs heavily against Jose Mourinho, who will leave Real Madrid this summer. Ferguson is understood to feel strongly that Moyes’ lack of Champions League experience is not an issue. He was deeply irritated when Moyes’ so-called “inexperience” was put to him by journalists in February.

Though there have been suggestions that the retirement story slipped out because of a TV programme about the United manager, scheduled for Sunday on the club’s in-house channel, senior sources maintain that today was always the planned announcement date, meaning an emotional last Old Trafford occasion for the Glaswegian when United entertain Swansea City on Sunday.

Before United were listed on the New York Stock Exchange last year, the club warned that “any successor to our current manager may not be as successful. A downturn in the performance of our first team could adversely affect our ability to attract and retain coaches and players.” The share price fluctuated, dropping 4.7 per cent in the first 10 minutes of trading.

United’s ambassador and former captain Bryan Robson said that the incoming manager had to win a trophy and play attractive football in his first season. “You’ve got to play… a passing game and also very attacking [football],” he said.

Ferguson, who will become an ambassador and director of United, told his players of his intentions at around 8.50am in what is understood to have been an emotional conversation.

He said in a statement: “It was important to me to leave an organisation in the strongest possible shape and I believe I have done so.”

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